Well. While we all thought our beloved Halo character, the Arbiter, was not, in fact, as Earthly as we all thought. Maybe he was an alien! People are getting stupider, maybe in the year 2556, no one could discern between humans and aliens. They could easily have mistaken the Arbiter for a human, or mutated goat. Think about it.
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What if the Arbiter was in fact a Samurai from ancient times that was transported to the future? And because of the way he looked everyone thought he was an alien. The Elites saw him as being one of their own and adopted and raised them as an elite. That is why he looks like an alien, because he is an alien.